OpenRaiser/Intern-Atlas huggingface dataset:
Towards scalable organ level 3D plant segmentation: Bridging the data algorithm computing gap
Venue: arXiv cs.CV 2025
Year: 2025

The precise characterization of plant morphology provides valuable insights into plant environment interactions and genetic evolution. A key technology for extracting this information is 3D segmentation, which delineates individual plant organs from complex point clouds. Despite significant progress in general 3D computer vision domains, the adoption of 3D segmentation for plant phenotyping remains limited by three major challenges: i) the scarcity of large-scale annotated datasets, ii) technical difficulties in adapting advanced deep neural networks to plant point clouds, and iii) the lack of standardized benchmarks and evaluation protocols tailored to plant science. This review systematically addresses these barriers by: i) providing an overview of existing 3D plant datasets in the context of general 3D segmentation domains, ii) systematically summarizing deep learning-based methods for point cloud semantic and instance segmentation, iii) introducing Plant Segmentation Studio (PSS), an open-source framework for reproducible benchmarking, and iv) conducting extensive quantitative experiments to evaluate representative networks and sim-to-real learning strategies. Our findings highlight the efficacy of sparse convolutional backbones and transformer-based instance segmentation, while also emphasizing the complementary role of modeling-based and augmentation-based synthetic data generation for sim-to-real learning in reducing annotation demands. In general, this study bridges the gap between algorithmic advances and practical deployment, providing immediate tools for researchers and a roadmap for developing data-efficient and generalizable deep learning solutions in 3D plant phenotyping. Data and code are available at https://github.com/perrydoremi/PlantSegStudio.
Embedding Poisoning: Bypassing Safety Alignment via Embedding Semantic Shift
Venue: arXiv cs.CR 2025
Year: 2025

The widespread distribution of Large Language Models (LLMs) through public platforms like Hugging Face introduces significant security challenges. While these platforms perform basic security scans, they often fail to detect subtle manipulations within the embedding layer. This work identifies a novel class of deployment phase attacks that exploit this vulnerability by injecting imperceptible perturbations directly into the embedding layer outputs without modifying model weights or input text. These perturbations, though statistically benign, systematically bypass safety alignment mechanisms and induce harmful behaviors during inference. We propose Search based Embedding Poisoning(SEP), a practical, model agnostic framework that introduces carefully optimized perturbations into embeddings associated with high risk tokens. SEP leverages a predictable linear transition in model responses, from refusal to harmful output to semantic deviation to identify a narrow perturbation window that evades alignment safeguards. Evaluated across six aligned LLMs, SEP achieves an average attack success rate of 96.43% while preserving benign task performance and evading conventional detection mechanisms. Our findings reveal a critical oversight in deployment security and emphasize the urgent need for embedding level integrity checks in future LLM defense strategies.
A Multi-Modal Deep Learning Framework for Colorectal Pathology Diagnosis: Integrating Histological and Colonoscopy Data in a Pilot Study
Venue: arXiv cs.CV 2025
Year: 2025

Colorectal diseases, including inflammatory conditions and neoplasms, require quick, accurate care to be effectively treated. Traditional diagnostic pipelines require extensive preparation and rely on separate, individual evaluations on histological images and colonoscopy footage, introducing possible variability and inefficiencies. This pilot study proposes a unified deep learning network that uses convolutional neural networks (CN N s) to classify both histopathological slides and colonoscopy video frames in one pipeline. The pipeline integrates class-balancing learning, robust augmentation, and calibration methods to ensure accurate results. Static colon histology images were taken from the PathMNIST dataset, and the lower gastrointestinal (colonoscopy) videos were drawn from the HyperKvasir dataset. The CNN architecture used was ResNet-50. This study demonstrates an interpretable and reproducible diagnostic pipeline that unifies multiple diagnostic modalities to advance and ease the detection of colorectal diseases.
Variational Garrote for Statistical Physics-based Sparse and Robust Variable Selection
Venue: arXiv cs.LG 2025
Year: 2025

Selecting key variables from high-dimensional data is increasingly important in the era of big data. Sparse regression serves as a powerful tool for this purpose by promoting model simplicity and explainability. In this work, we revisit a valuable yet underutilized method, the statistical physics-based Variational Garrote (VG), which introduces explicit feature selection spin variables and leverages variational inference to derive a tractable loss function. We enhance VG by incorporating modern automatic differentiation techniques, enabling scalable and efficient optimization. We evaluate VG on both fully controllable synthetic datasets and complex real-world datasets. Our results demonstrate that VG performs especially well in highly sparse regimes, offering more consistent and robust variable selection than Ridge and LASSO regression across varying levels of sparsity. We also uncover a sharp transition: as superfluous variables are admitted, generalization degrades abruptly and the uncertainty of the selection variables increases. This transition point provides a practical signal for estimating the correct number of relevant variables, an insight we successfully apply to identify key predictors in real-world data. We expect that VG offers strong potential for sparse modeling across a wide range of applications, including compressed sensing and model pruning in machine learning.
MeanFlow-Accelerated Multimodal Video-to-Audio Synthesis via One-Step Generation
Venue: arXiv cs.SD 2025
Year: 2025

A key challenge in synthesizing audios from silent videos is the inherent trade-off between synthesis quality and inference efficiency in existing methods. For instance, flow matching based models rely on modeling instantaneous velocity, inherently require an iterative sampling process, leading to slow inference speeds. To address this efficiency bottleneck, we introduce a MeanFlow-accelerated model that characterizes flow fields using average velocity, enabling one-step generation and thereby significantly accelerating multimodal video-to-audio (VTA) synthesis while preserving audio quality, semantic alignment, and temporal synchronization. Furthermore, a scalar rescaling mechanism is employed to balance conditional and unconditional predictions when classifier-free guidance (CFG) is applied, effectively mitigating CFG-induced distortions in one step generation. Since the audio synthesis network is jointly trained with multimodal conditions, we further evaluate it on text-to-audio (TTA) synthesis task. Experimental results demonstrate that incorporating MeanFlow into the network significantly improves inference speed without compromising perceptual quality on both VTA and TTA synthesis tasks.
AI-based response assessment and prediction in longitudinal imaging for brain metastases treated with stereotactic radiosurgery
Venue: arXiv cs.CV 2025
Year: 2025

Brain Metastases (BM) are a large contributor to mortality of patients with cancer. They are treated with Stereotactic Radiosurgery (SRS) and monitored with Magnetic Resonance Imaging (MRI) at regular follow-up intervals according to treatment guidelines. Analyzing and quantifying this longitudinal imaging represents an intractable workload for clinicians. As a result, follow-up images are not annotated and merely assessed by observation. Response to treatment in longitudinal imaging is being studied, to better understand growth trajectories and ultimately predict treatment success or toxicity as early as possible. In this study, we implement an automated pipeline to curate a large longitudinal dataset of SRS treatment data, resulting in a cohort of 896 BMs in 177 patients who were monitored for >360 days at approximately two-month intervals at Lausanne University Hospital (CHUV). We use a data-driven clustering to identify characteristic trajectories. In addition, we predict 12 months lesion-level response using classical as well as graph machine learning Graph Machine Learning (GML). Clustering revealed 5 dominant growth trajectories with distinct final response categories. Response prediction reaches up to 0.90 AUC (CI95%=0.88-0.92) using only pre-treatment and first follow-up MRI with gradient boosting. Similarly, robust predictive performance of up to 0.88 AUC (CI95%=0.86-0.90) was obtained using GML, offering more flexibility with a single model for multiple input time-points configurations. Our results suggest potential automation and increased precision for the comprehensive assessment and prediction of BM response to SRS in longitudinal MRI. The proposed pipeline facilitates scalable data curation for the investigation of BM growth patterns, and lays the foundation for clinical decision support systems aiming at optimizing personalized care.
Do LLMs exhibit the same commonsense capabilities across languages?
Venue: arXiv cs.CL 2025
Year: 2025

This paper explores the multilingual commonsense generation abilities of Large Language Models (LLMs). To facilitate this investigation, we introduce MULTICOM, a novel benchmark that extends the COCOTEROS dataset to four languages: English, Spanish, Dutch, and Valencian. The task involves generating a commonsensical sentence that includes a given triplet of words. We evaluate a range of open-source LLMs, including LLaMA, Qwen, Gemma, EuroLLM, and Salamandra, on this benchmark. Our evaluation combines automatic metrics, LLM-as-a-judge approaches (using Prometheus and JudgeLM), and human annotations. Results consistently show superior performance in English, with significantly lower performance in less-resourced languages. While contextual support yields mixed results, it tends to benefit underrepresented languages. These findings underscore the current limitations of LLMs in multilingual commonsense generation. The dataset is publicly available at https://huggingface.co/datasets/gplsi/MULTICOM.
Compare: A Framework for Scientific Comparisons
Venue: arXiv cs.DL 2025
Year: 2025

Navigating the vast and rapidly increasing sea of academic publications to identify institutional synergies, benchmark research contributions and pinpoint key research contributions has become an increasingly daunting task, especially with the current exponential increase in new publications. Existing tools provide useful overviews or single-document insights, but none supports structured, qualitative comparisons across institutions or publications. To address this, we demonstrate Compare, a novel framework that tackles this challenge by enabling sophisticated long-context comparisons of scientific contributions. Compare empowers users to explore and analyze research overlaps and differences at both the institutional and publication granularity, all driven by user-defined questions and automatic retrieval over online resources. For this we leverage on Retrieval-Augmented Generation over evolving data sources to foster long context knowledge synthesis. Unlike traditional scientometric tools, Compare goes beyond quantitative indicators by providing qualitative, citation-supported comparisons.
VQualA 2025 Challenge on Image Super-Resolution Generated Content Quality Assessment: Methods and Results
Venue: arXiv cs.CV 2025
Year: 2025

This paper presents the ISRGC-Q Challenge, built upon the Image Super-Resolution Generated Content Quality Assessment (ISRGen-QA) dataset, and organized as part of the Visual Quality Assessment (VQualA) Competition at the ICCV 2025 Workshops. Unlike existing Super-Resolution Image Quality Assessment (SR-IQA) datasets, ISRGen-QA places a greater emphasis on SR images generated by the latest generative approaches, including Generative Adversarial Networks (GANs) and diffusion models. The primary goal of this challenge is to analyze the unique artifacts introduced by modern super-resolution techniques and to evaluate their perceptual quality effectively. A total of 108 participants registered for the challenge, with 4 teams submitting valid solutions and fact sheets for the final testing phase. These submissions demonstrated state-of-the-art (SOTA) performance on the ISRGen-QA dataset. The project is publicly available at: https://github.com/Lighting-YXLI/ISRGen-QA.
Anticipating AMOC transitions via deep learning
Venue: arXiv cs.CE 2025
Year: 2025

Key components of the Earth system can undergo abrupt and potentially irreversible transitions when the magnitude or rate of external forcing exceeds critical thresholds. In this study, we use the example of the Atlantic Meridional Overturning Circulation (AMOC) to demonstrate the challenges associated with anticipating such transitions when the system is susceptible to bifurcation-induced, rate-induced, and noise-induced tipping. Using a calibrated AMOC box model, we conduct large ensemble simulations and show that transition behavior is inherently probabilistic: under identical freshwater forcing scenarios, some ensemble members exhibit transitions while others do not. In this stochastic regime, traditional early warning indicators based on critical slowing down are unreliable in predicting impending transitions. To address this limitation, we develop a convolutional neural network (CNN)-based approach that identifies higher-order statistical differences between transitioning and non-transitioning trajectories within the ensemble realizations. This method enables the real-time prediction of transition probabilities for individual trajectories prior to the onset of tipping. Our results show that the CNN-based indicator provides effective early warnings in a system where transitions can be induced by bifurcations, critical forcing rates, and noise. These findings underscore the potential in identifying safe operating spaces and early warning indicators for abrupt transitions of Earth system components under uncertainty.
IGAff: Benchmarking Adversarial Iterative and Genetic Affine Algorithms on Deep Neural Networks
Venue: arXiv cs.CV 2025
Year: 2025

Deep neural networks currently dominate many fields of the artificial intelligence landscape, achieving state-of-the-art results on numerous tasks while remaining hard to understand and exhibiting surprising weaknesses. An active area of research focuses on adversarial attacks, which aim to generate inputs that uncover these weaknesses. However, this proves challenging, especially in the black-box scenario where model details are inaccessible. This paper explores in detail the impact of such adversarial algorithms on ResNet-18, DenseNet-121, Swin Transformer V2, and Vision Transformer network architectures. Leveraging the Tiny ImageNet, Caltech-256, and Food-101 datasets, we benchmark two novel black-box iterative adversarial algorithms based on affine transformations and genetic algorithms: 1) Affine Transformation Attack (ATA), an iterative algorithm maximizing our attack score function using random affine transformations, and 2) Affine Genetic Attack (AGA), a genetic algorithm that involves random noise and affine transformations. We evaluate the performance of the models in the algorithm parameter variation, data augmentation, and global and targeted attack configurations. We also compare our algorithms with two black-box adversarial algorithms, Pixle and Square Attack. Our experiments yield better results on the image classification task than similar methods in the literature, achieving an accuracy improvement of up to 8.82%. We provide noteworthy insights into successful adversarial defenses and attacks at both global and targeted levels, and demonstrate adversarial robustness through algorithm parameter variation.
FSG-Net: Frequency-Spatial Synergistic Gated Network for High-Resolution Remote Sensing Change Detection
Venue: arXiv cs.CV 2025
Year: 2025

Change detection from high-resolution remote sensing images lies as a cornerstone of Earth observation applications, yet its efficacy is often compromised by two critical challenges. First, false alarms are prevalent as models misinterpret radiometric variations from temporal shifts (e.g., illumination, season) as genuine changes. Second, a non-negligible semantic gap between deep abstract features and shallow detail-rich features tends to obstruct their effective fusion, culminating in poorly delineated boundaries. To step further in addressing these issues, we propose the Frequency-Spatial Synergistic Gated Network (FSG-Net), a novel paradigm that aims to systematically disentangle semantic changes from nuisance variations. Specifically, FSG-Net first operates in the frequency domain, where a Discrepancy-Aware Wavelet Interaction Module (DAWIM) adaptively mitigates pseudo-changes by discerningly processing different frequency components. Subsequently, the refined features are enhanced in the spatial domain by a Synergistic Temporal-Spatial Attention Module (STSAM), which amplifies the saliency of genuine change regions. To finally bridge the semantic gap, a Lightweight Gated Fusion Unit (LGFU) leverages high-level semantics to selectively gate and integrate crucial details from shallow layers. Comprehensive experiments on the CDD, GZ-CD, and LEVIR-CD benchmarks validate the superiority of FSG-Net, establishing a new state-of-the-art with F1-scores of 94.16%, 89.51%, and 91.27%, respectively. The code will be made available at https://github.com/zxXie-Air/FSG-Net after a possible publication.
WS$^2$: Weakly Supervised Segmentation using Before-After Supervision in Waste Sorting
Venue: arXiv cs.CV 2025
Year: 2025

In industrial quality control, to visually recognize unwanted items within a moving heterogeneous stream, human operators are often still indispensable. Waste-sorting stands as a significant example, where operators on multiple conveyor belts manually remove unwanted objects to select specific materials. To automate this recognition problem, computer vision systems offer great potential in accurately identifying and segmenting unwanted items in such settings. Unfortunately, considering the multitude and the variety of sorting tasks, fully supervised approaches are not a viable option to address this challange, as they require extensive labeling efforts. Surprisingly, weakly supervised alternatives that leverage the implicit supervision naturally provided by the operator in his removal action are relatively unexplored. In this paper, we define the concept of Before-After Supervision, illustrating how to train a segmentation network by leveraging only the visual differences between images acquired \textit{before} and \textit{after} the operator. To promote research in this direction, we introduce WS$^2$ (Weakly Supervised segmentation for Waste-Sorting), the first multiview dataset consisting of more than 11 000 high-resolution video frames captured on top of a conveyor belt, including "before" and "after" images. We also present a robust end-to-end pipeline, used to benchmark several state-of-the-art weakly supervised segmentation methods on WS$^2$.
Signal-Based Malware Classification Using 1D CNNs
Venue: arXiv cs.CR 2025
Year: 2025

Malware classification is a contemporary and ongoing challenge in cyber-security: modern obfuscation techniques are able to evade traditional static analysis, while dynamic analysis is too resource intensive to be deployed at a large scale. One prominent line of research addresses these limitations by converting malware binaries into 2D images by heuristically reshaping them into a 2D grid before resizing using Lanczos resampling. These images can then be classified based on their textural information using computer vision approaches. While this approach can detect obfuscated malware more effectively than static analysis, the process of converting files into 2D images results in significant information loss due to both quantisation noise, caused by rounding to integer pixel values, and the introduction of 2D dependencies which do not exist in the original data. This loss of signal limits the classification performance of the downstream model. This work addresses these weaknesses by instead resizing the files into 1D signals which avoids the need for heuristic reshaping, and additionally these signals do not suffer from quantisation noise due to being stored in a floating-point format. It is shown that existing 2D CNN architectures can be readily adapted to classify these 1D signals for improved performance. Furthermore, a bespoke 1D convolutional neural network, based on the ResNet architecture and squeeze-and-excitation layers, was developed to classify these signals and evaluated on the MalNet dataset. It was found to achieve state-of-the-art performance on binary, type, and family level classification with F1 scores of 0.874, 0.503, and 0.507, respectively, paving the way for future models to operate on the proposed signal modality.
PAC-Bayesian Generalization Bounds for Graph Convolutional Networks on Inductive Node Classification
Venue: arXiv cs.LG 2025
Year: 2025

Graph neural networks (GNNs) have achieved remarkable success in processing graph-structured data across various applications. A critical aspect of real-world graphs is their dynamic nature, where new nodes are continually added and existing connections may change over time. Previous theoretical studies, largely based on the transductive learning framework, fail to adequately model such temporal evolution and structural dynamics. In this paper, we presents a PAC-Bayesian theoretical analysis of graph convolutional networks (GCNs) for inductive node classification, treating nodes as dependent and non-identically distributed data points. We derive novel generalization bounds for one-layer GCNs that explicitly incorporate the effects of data dependency and non-stationarity, and establish sufficient conditions under which the generalization gap converges to zero as the number of nodes increases. Furthermore, we extend our analysis to two-layer GCNs, and reveal that it requires stronger assumptions on graph topology to guarantee convergence. This work establishes a theoretical foundation for understanding and improving GNN generalization in dynamic graph environments.